Contacts of the helix formed by residues 696 - 710 (chain A) in PDB entry 6DGD
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 696 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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694A HIS* 3.0 23.7 + - - -
695A PRO* 1.3 78.4 - - - +
697A ARG* 1.3 65.4 + - - +
698A VAL* 3.7 8.3 + - - +
699A ARG* 3.2 24.3 + - - +
700A LEU* 3.2 20.3 + - - +
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Residues in contact with ARG 697 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A TRP* 3.7 28.7 - - - +
86A TYR* 3.4 41.8 - - + +
634A SER* 3.5 27.1 + - - +
695A PRO 4.1 1.2 + - - -
696A SER* 1.3 73.4 + - - +
698A VAL* 1.3 85.4 - - - +
700A LEU* 3.6 6.6 + - + +
701A GLN* 3.0 25.9 + - - +
727A ASP* 4.9 1.1 - - - -
809A SO4 2.9 52.1 + - - +
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Residues in contact with VAL 698 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A TRP* 5.9 0.9 - - - +
696A SER* 3.3 6.5 - - - +
697A ARG* 1.3 109.6 - - - +
699A ARG* 1.3 64.4 + - + +
701A GLN* 3.3 17.5 - - - +
702A HIS* 2.8 48.2 + - + +
809A SO4 5.2 1.3 - - - +
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Residues in contact with ARG 699 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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664A LEU* 3.0 53.6 + - - +
665A ALA 5.1 0.2 + - - -
666A ASP* 3.3 27.3 + - - +
694A HIS* 3.5 21.5 - - + +
696A SER* 3.2 27.8 + - - +
698A VAL* 1.3 79.5 - - + +
700A LEU* 1.3 58.9 + - - +
702A HIS* 3.0 11.9 + - - +
703A ILE* 2.8 35.2 + - + +
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Residues in contact with LEU 700 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A TYR* 6.2 2.2 - - + -
88A HIS* 6.1 0.4 - - + -
634A SER* 4.3 12.6 - - - +
635A HIS 4.8 2.9 - - - +
636A VAL* 3.4 29.8 - - + -
669A LEU* 4.6 5.4 - - + -
692A LEU* 4.1 15.5 - - + +
693A GLN* 3.9 24.7 - - - +
694A HIS* 3.8 26.2 + - + +
696A SER 3.2 14.2 + - - +
697A ARG* 3.9 6.3 - - + +
699A ARG* 1.3 75.8 - - - +
701A GLN* 1.3 69.4 + - - +
703A ILE* 3.5 13.0 - - + +
704A VAL* 3.0 32.7 + - + +
726A VAL* 5.6 2.0 - - + -
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Residues in contact with GLN 701 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A TRP* 4.5 13.1 + - - +
85A GLU* 3.7 13.2 + - - +
86A TYR* 3.4 49.8 - - + +
88A HIS* 3.7 17.2 + - + +
697A ARG* 3.0 18.4 + - - +
698A VAL* 3.1 28.0 + - - +
700A LEU* 1.3 79.0 - - - +
702A HIS* 1.3 67.7 + - - +
704A VAL* 3.7 3.2 + - - +
705A SER* 2.9 35.4 + - - -
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Residues in contact with HIS 702 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662A SER* 5.3 0.2 + - - -
664A LEU* 4.4 28.6 - - + +
698A VAL* 2.8 38.3 + - + +
699A ARG* 3.4 10.3 - - - +
701A GLN* 1.3 84.4 - - - +
703A ILE* 1.3 66.5 + - - +
705A SER* 3.9 5.8 - - - -
706A GLY* 2.9 21.0 + - - -
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Residues in contact with ILE 703 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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659A LEU* 4.2 16.2 - - + +
662A SER* 4.1 24.6 + - - +
664A LEU* 3.9 36.3 - - + +
665A ALA* 4.3 1.6 - - - +
669A LEU* 4.0 39.3 - - + -
692A LEU* 5.7 0.9 - - + -
694A HIS* 4.5 4.3 - - + -
699A ARG* 2.8 27.0 + - + +
700A LEU* 3.2 18.1 + - + +
702A HIS* 1.3 77.2 - - - +
704A VAL* 1.3 65.2 + - + +
706A GLY* 4.0 0.3 - - - -
707A THR* 2.9 27.4 + - - -
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Residues in contact with VAL 704 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A HIS* 3.1 39.0 - - + +
636A VAL* 4.9 7.9 - - + -
638A ILE* 5.6 3.6 - - + -
659A LEU* 3.9 14.8 - - + -
692A LEU* 3.4 33.7 - - + -
700A LEU* 3.0 22.4 + - + +
701A GLN* 3.7 0.4 - - - +
703A ILE* 1.3 75.6 - - + +
705A SER* 1.3 60.1 + - - +
707A THR* 3.6 0.4 - - - -
708A LEU* 2.8 39.5 + - + +
724A LEU* 5.2 5.6 - - + -
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Residues in contact with SER 705 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A GLU* 2.7 29.2 + - - -
88A HIS* 4.2 11.7 - - - -
701A GLN* 2.9 26.5 + - - -
702A HIS* 3.9 7.9 - - - -
703A ILE 3.3 0.2 - - - -
704A VAL* 1.3 78.7 - - - +
706A GLY* 1.3 61.4 + - - +
708A LEU* 3.4 9.6 + - - +
709A ALA* 3.6 10.4 + - - +
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Residues in contact with GLY 706 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662A SER* 6.0 0.7 - - - -
664A LEU* 6.5 0.4 - - - -
702A HIS 2.9 16.2 + - - -
703A ILE 4.0 0.7 - - - -
705A SER* 1.3 74.8 - - - +
707A THR* 1.3 62.3 + - - +
708A LEU 3.1 0.9 + - - -
709A ALA* 3.3 8.7 + - - +
710A LEU* 3.2 24.8 - - - +
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Residues in contact with THR 707 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655A LEU* 4.8 7.9 - - + -
658A LEU* 3.7 33.9 + - + +
659A LEU* 3.6 34.8 - - + +
662A SER* 4.0 17.3 + - - -
703A ILE 2.9 19.0 + - - -
704A VAL 3.8 2.2 - - - -
706A GLY* 1.3 75.9 - - - +
708A LEU* 1.3 63.3 + - + +
710A LEU* 3.4 22.5 + - - +
711A ILE* 3.9 3.7 + - + +
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Residues in contact with LEU 708 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A HIS* 3.9 23.6 - - + +
638A ILE* 6.3 2.5 - - + -
655A LEU* 5.6 6.3 - - + -
704A VAL* 2.8 24.7 + - + +
705A SER* 3.7 6.3 - - - +
706A GLY 3.1 0.6 - - - -
707A THR* 1.3 75.9 - - + +
709A ALA* 1.3 65.9 + - - +
710A LEU 3.0 2.9 + - - -
711A ILE* 3.2 42.3 + - + +
722A TRP* 4.6 19.3 - - + -
724A LEU* 3.8 28.7 - - + -
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Residues in contact with ALA 709 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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705A SER 3.6 6.8 + - - +
706A GLY* 3.3 11.6 + - - +
708A LEU* 1.3 77.7 - - - +
710A LEU* 1.3 64.6 + - + +
711A ILE* 3.6 2.6 + - - +
712A ASN* 4.8 9.4 + - - -
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Residues in contact with LEU 710 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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658A LEU* 4.0 19.0 - - + +
706A GLY 3.2 21.5 - - - +
707A THR* 3.4 11.3 + - - +
708A LEU 3.0 0.6 - - - -
709A ALA* 1.3 87.0 - - + +
711A ILE* 1.3 56.8 + - - -
712A ASN* 3.3 3.4 - - - +
713A THR* 3.0 39.0 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il